Why to not liftover SNPS

[Mireia Marín Ginestar]

Hello!

I'm benchmarking different tools and trying to understand what they do different. 

I'd like to understand why the Liftover Tool should, specifically, not be used for SNPs. Do you expect SNPs uncorrectly lifted or a higher drop out ratio?

Thanks for your attention and sorry if it's been asked before. 

Thanks again, 
Mireia

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

When attempting to convert small regions between assemblies, the resulting alignment may not score high enough to be considered a successful conversion. We used to get many questions asking why their SNP was not found in the target assembly, and we created the following FAQ to address these questions:

https://genome.ucsc.edu/FAQ/FAQreleases.html#snpConversion

We recommend searching for the rsID in the target assembly, as rsIDs are intended to be stable across genome assemblies, despite changes in genomic positions.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

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